Check-in and the yukata
Ryokan check-in tends to run earlier in the afternoon than a standard hotel, and shortly after arriving you'll usually be given a yukata — a simple cotton robe — to wear around the property for the rest of your stay, including to dinner. Wearing it is expected, not optional politeness.
Dinner and the futon swap
Kaiseki, a multi-course seasonal dinner, is often served at a set time either in your room or a dining area, and it's worth not filling up beforehand — the courses add up. While you're at dinner, staff typically enter the room to lay out futon bedding on the tatami floor in place of the low table used earlier in the evening.
Bathing
Many ryokan, particularly those built around a hot spring, have communal or private onsen baths following the same etiquette as a public sento — wash thoroughly before entering the shared water, and bathe without swimwear.
A slower pace, on purpose
A ryokan stay is built around slowing down rather than efficiency, and it works best when treated that way — as an evening to spend at the property rather than a base to drop bags at before heading straight back out.